Soybean variety XB39N05

ABSTRACT

According to the invention, there is provided a novel soybean variety designated XB39N05. This invention thus relates to the seeds of soybean variety XB39N05, to the plants of soybean XB39N05 to plant parts of soybean variety XB39N05 and to methods for producing a soybean plant produced by crossing plants of the soybean variety XB39N05 with another soybean plant, using XB39N05 as either the male or the female parent.

FIELD OF INVENTION

This invention is in the field of soybean breeding, specificallyrelating to a soybean variety designated XB39N05.

BACKGROUND OF INVENTION

The present invention relates to a new and distinctive soybean variety,designated XB39N05 which has been the result of years of carefulbreeding and selection as part of a soybean breeding program. There arenumerous steps in the development of any novel, desirable plantgermplasm. Plant breeding begins with the analysis and definition ofproblems and weaknesses of the current germplasm, the establishment ofprogram goals, and the definition of specific breeding objectives. Thenext step is selection of germplasm that possess the traits to meet theprogram goals. The goal is to combine in a single variety an improvedcombination of desirable traits from the parental germplasm. Theseimportant traits may include but are not limited to higher seed yield,resistance to diseases and insects, tolerance to drought and heat, andbetter agronomic qualities.

These processes, which lead to the final step of marketing anddistribution, can take from six to twelve years from the time the firstcross is made. Therefore, development of new varieties is atime-consuming process that requires precise forward planning, efficientuse of resources, and a minimum of changes in direction.

Soybean (Glycine max), is an important and valuable field crop. Thus, acontinuing goal of soybean breeders is to develop stable, high yieldingsoybean varieties that are agronomically sound. The reasons for thisgoal are to maximize the amount of grain produced on the land used andto supply food for both animals and humans. To accomplish this goal, thesoybean breeder must select and develop soybean plants that have thetraits that result in superior varieties.

Pioneer soybean research staff create over 500,000 potential newvarieties each year. Of those new varieties, less than 50 and morecommonly less than 25 are actually selected for commercial use.

The soybean is the world's leading source of vegetable oil and proteinmeal. The oil extracted from soybeans is used for cooking oil,margarine, and salad dressings. Soybean oil is composed of saturated,monounsaturated and polyunsaturated fatty acids. It has a typicalcomposition of 11% palmitic, 4% stearic, 25% oleic, 50% linoleic and 9%linolenic fatty acid content (“Economic Implications of Modified SoybeanTraits Summary Report”, Iowa Soybean Promotion Board & American SoybeanAssociation Special Report 92S, May 1990). Changes in fatty acidcomposition for improved oxidative stability and nutrition are alsoimportant traits. Industrial uses for processed soybean oil includeingredients for paints, plastics, fibers, detergents, cosmetics, andlubricants. Soybean oil may be split, inter-esterified, sulfurized,epoxidized, polymerized, ethoxylated, or cleaved. Designing andproducing soybean oil derivatives with improved functionality,oliochemistry, is a rapidly growing field. The typical mixture oftriglycerides is usually split and separated into pure fatty acids,which are then combined with petroleum-derived alcohols or acids,nitrogen, sulfonates, chlorine, or with fatty alcohols derived from fatsand oils.

Soybean is also used as a food source for both animals and humans.Soybean is widely used as a source of protein for animal feeds forpoultry, swine and cattle. During processing of whole soybeans, thefibrous hull is removed and the oil is extracted. The remaining soybeanmeal is a combination of carbohydrates and approximately 50% protein.

For human consumption soybean meal is made into soybean flour which isprocessed to protein concentrates used for meat extenders or specialtypet foods. Production of edible protein ingredients from soybean offersa healthy, less expensive replacement for animal protein in meats aswell as dairy-type products.

SUMMARY OF INVENTION

According to the invention, there is provided a novel soybean variety,designated XB39N05. This invention thus relates to the seeds of soybeanvariety XB39N05, to the plants of soybean XB39N05, to plant parts ofsoybean variety XB39N05 and to methods for producing a soybean plantproduced by crossing soybean variety XB39N05 with another soybean plant,using XB39N05 as either the male or the female parent. This inventionalso relates to methods for introgressing a transgenic or mutant traitinto soybean variety XB39N05 and to the soybean plants and plant partsproduced by those methods. This invention also relates to soybeanvarieties or breeding varieties and plant parts derived from soybeanvariety XB39N05, to methods for producing other soybean varieties orplant parts derived from soybean variety XB39N05 and to the soybeanplants, varieties, and their parts derived from use of those methods.This invention further relates to soybean seeds, plants, and plant partsproduced by crossing the soybean variety XB39N05 with another soybeanvariety.

Definitions

Certain definitions used in the specification are provided below. Alsoin the examples which follow, a number of terms are used. In order toprovide a clear and consistent understanding of the specification andclaims, including the scope to be given such terms, the followingdefinitions are provided:

ALLELE. Any of one or more alternative forms of a genetic sequence. In adiploid cell or organism, the two alleles of a given sequence typicallyoccupy corresponding loci on a pair of homologous chromosomes.

ALTER. The utilization of up-regulation, down-regulation, or genesilencing.

ANTHESIS. The time of a flower's opening.

BACKCROSSING. Process in which a breeder crosses a progeny variety backto one of the parental genotypes one or more times.

BREEDING. The genetic manipulation of living organisms.

BREEDING CROSS. A cross to introduce new genetic material into a plantfor the development of a new variety. For example, one could cross plantA with plant B, wherein plant B would be genetically different fromplant A. After the breeding cross, the resulting F1 plants could then beselfed or sibbed for one, two, three or more times (F1, F2, F3, etc.)until a new variety is developed. For clarification, such new varietywould be within a pedigree distance of one breeding cross of plants Aand B. The process described above would be referred to as one breedingcycle.

BU/A=Bushels per Acre. The seed yield in bushels/acre is the actualyield of the grain at harvest.

BSR=Brown Stem Rot Tolerance. This is a visual disease score from 1 to 9comparing all genotypes in a given test. The score is based on leafsymptoms of yellowing and necrosis caused by brown stem rot. A score of9 indicates no symptoms. Visual scores range down to a score of 1 whichindicates severe symptoms of leaf yellowing and necrosis.

CELL. Cell as used herein includes a plant cell, whether isolated, intissue culture or incorporated in a plant or plant part.

CW=Canopy Width. This is visual observation of the canopy width from 1to 9 comparing all genotypes in a given test. The higher the score thebetter the canopy width observed.

CNKR=Stem Canker Tolerance. This is a visual disease score from 1 to 9comparing all genotypes in a given test. The score is based uponpremature plant death. A score of 9 indicates no symptoms, whereas ascore of 1 indicates the entire experimental unit died very early.

COTYLEDON. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

ELITE VARIETY. A variety that is sufficiently homozygous and homogeneousto be used for commercial grain production. An elite variety may also beused in further breeding.

EMBRYO. The embryo is the small plant contained within a mature seed.

EMGSC=Emergence Score. The percentage of emerged plants in a plotrespective to the number of seeds planted.

F3 This symbol denotes a generation resulting from the selfing of the F2generation along with selection for type and rogueing of off-types. The“F” number is a term commonly used in genetics, and designates thenumber of the filial generation. The “F3” generation denotes theoffspring resulting from the selfing or self mating of members of thegeneration having the next lower “F” number, viz. the F2 generation.

FEC=Iron-deficiency Chlorosis. Plants are scored 1 to 9 based on visualobservations. A score of 1 indicates the plants are dead or dying fromiron-deficiency chlorosis, a score of 5 means plants have intermediatehealth with some leaf yellowing and a score of 9 means no stunting ofthe plants or yellowing of the leaves. Plots are usually scored in midJuly.

FECL=Iron-deficiency Chlorosis. Plants are scored 1 to 9 based on visualobservations. A score of 1 indicates the plants are dead or dying fromiron-deficiency chlorosis, a score of 5 means plants have intermediatehealth with some leaf yellowing and a score of 9 means no stunting ofthe plants or yellowing of the leaves. Plots are scored around midAugust.

FEY=Frogeye Tolerance. This is a visual disease score from 1 to 9comparing all genotypes in a given test. The score is based upon leaflesions. A score of 9 indicates no lesions, whereas a score of 1indicates severe leaf necrosis.

GENE SILENCING. The interruption or suppression of the expression of agene at the level of transcription or translation.

GENOTYPE. Refers to the genetic constitution of a cell or organism.

HABIT. This refers to the physical appearance of a plant. It can bedeterminate, semi-determinate, intermediate, or indeterminate. Insoybeans, indeterminate varieties are those in which stem growth is notlimited by formation of a reproductive structure (i.e., flowers, podsand seeds) and hence growth continues throughout flowering and duringpart of pod filling. The main stem will develop and set pods over aprolonged period under favorable conditions. In soybeans, determinatevarieties are those in which stem growth ceases at flowering time. Mostflowers develop simultaneously, and most pods fill at approximately thesame time. The terms semi-determinate and intermediate are also used todescribe plant habit and are defined in Bernard, R. L. 1972. “Two genesaffecting stem termination in soybeans.” Crop Science 12:235–239;Woodworth, C. M. 1932. “Genetics and breeding in the improvement of thesoybean.” Bull. Agric. Exp. Stn. (Illinois) 384:297–404; Woodworth, C.M. 1933. “Genetics of the soybean.” J. Am. Soc. Agron. 25:36–51.

HERBRES=Herbicide Resistance. This indicates that the plant is moretolerant to the herbicide shown than the level of herbicide toleranceexhibited by wild type plants. A designation of RR indicates toleranceto glyphosate and a designation of STS indicates tolerance tosulfonylurea herbicides.

HGT=Plant Height. Plant height is taken from the top of the soil to toppod of the plant and is measured in inches.

HILUM. This refers to the scar left on the seed which marks the placewhere the seed was attached to the pod prior to it (the seed) beingharvested.

HYPL=Hypocotyl Elongation. This score indicates the ability of the seedto emerge when planted 3″ deep in sand pots and with a controlledtemperature of 25° C. The number of plants that emerge each day arecounted. Based on this data, each genotype is given a 1 to 9 score basedon its rate of emergence and percent of emergence. A score of 9indicates an excellent rate and percent of emergence, an intermediatescore of 5 indicates average ratings and a 1 score indicates a very poorrate and percent of emergence.

HYPOCOTYL. A hypocotyl is the portion of an embryo or seedling betweenthe cotyledons and the root. Therefore, it can be considered atransition zone between shoot and root.

LDGSEV=Lodging Resistance. Lodging is rated on a scale of 1 to 9. Ascore of 9 indicates erect plants. A score of 5 indicates plants areleaning at a 45° angle in relation to the ground and a score of 1indicates plants are laying on the ground.

LEAFLETS. These are part of the plant shoot, and they manufacture foodfor the plant by the process of photosynthesis.

LINKAGE. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

LINKAGE DISEQUILIBRIUM. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

LLE=Linoleic Acid Percent. Linoleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LLN=Linolenic Acid Percent. Linolenic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LOCUS. A defined segment of DNA.

MAT ABS=Absolute Maturity. This term is defined as the length of timefrom planting to complete physiological development (maturity). Theperiod from planting until maturity is reached is measured in days,usually in comparison to one or more standard varieties. Plants areconsidered mature when 95% of the pods have reached their mature color.

MATURITY GROUP. This refers to an agreed-on industry division of groupsof varieties, based on the zones in which they are adapted primarilyaccording to day length or latitude. They consist of very long daylength varieties (Groups 000, 00, 0), and extend to very short daylength varieties (Groups VII, VIII, IX, X).

OIL=Oil Percent. Soybean seeds contain a considerable amount of oil. Oilis measured by NIR spectrophotometry, and is reported on an as ispercentage basis.

OLC=Oleic Acid Percent. Oleic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

PEDIGREE DISTANCE. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

PERCENT IDENTITY. Percent identity as used herein refers to thecomparison of the homozygous alleles of two soybean varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between soybean variety 1 and soybean variety 2means that the two varieties have the same allele at 90% of their loci.

PERCENT SIMILARITY. Percent similarity as used herein refers to thecomparison of the homozygous alleles of a soybean variety such asXB39N05 with another plant, and if the homozygous allele of XB39N05matches at least one of the alleles from the other plant then they arescored as similar. Percent similarity is determined by comparing astatistically significant number of loci and recording the number ofloci with similar alleles as a percentage. A percent similarity of 90%between XB39N05 and another plant means that XB39N05 matches at leastone of the alleles of the other plant at 90% of the loci.

PLANT. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Seed or embryo that will produce theplant is also considered to be the plant.

PLANT PARTS. As used herein, the term “plant parts” includes leaves,stems, roots, root tips, anthers, seed, grain, embryo, pollen, ovules,flowers, cotyledon, hypocotyl, pod, flower, shoot and stalk, tissue,cells and the like.

PLM=Palmitic Acid Percent. Palmitic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

POD. This refers to the fruit of a soybean plant. It consists of thehull or shell (pericarp) and the soybean seeds.

PRT=Phytophthora Tolerance. Tolerance to Phytophthora root rot is ratedon a scale of 1 to 9, with a score of 9 being the best or highesttolerance ranging down to a score of 1 which indicates the plants haveno tolerance to Phytophthora.

PRMMAT=Predicted Relative Maturity. Soybean maturities are divided intorelative maturity groups. In the United States the most common maturitygroups are 00 through VIII. Within maturity groups 00 through V aresub-groups. A sub-group is a tenth of a relative maturity group. Withinnarrow comparisons, the difference of a tenth of a relative maturitygroup equates very roughly to a day difference in maturity at harvest.

PRO=Protein Percent. Soybean seeds contain a considerable amount ofprotein. Protein is generally measured by NIR spectrophotometry, and isreported on a dry weight basis.

PUBESCENCE. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and pods of the soybean plant.

RESISTANCE. Synonymous with tolerance. The ability of a plant towithstand exposure to an insect, disease, herbicide or other condition.A resistant plant variety will have a level of resistance higher than acomparable wild-type variety.

RKI=Root-knot Nematode, Southern. This is a visual disease score from 1to 9 comparing all genotypes in a given test. The score is based upondigging plants to visually score the roots for presence or absence ofgalling. A score of 9 indicates that there is no galling of the roots, ascore of 1 indicates large severe galling cover most of the root systemwhich results in pre-mature death from decomposing of the root system.

RKA=Root-knot Nematode, Peanut. This is a visual disease score from 1 to9 comparing all genotypes in a given test. The score is based upondigging plants to look at the roots for presence or absence of galling.A score of 9 indicates that there is no galling of the roots, a score of1 indicates large severe galling cover most of the root system whichresults in pre-mature death from decomposing of the root system.

SCN=Soybean Cyst Nematode Resistance. The score is based on resistanceto a particular race of soybean cyst nematode, such as race 1, 2, 3, 5or 14. Scores are visual observations of resistance as versus othergenotypes in the test, with a higher score indicating a higher level ofresistance.

SD VIG=Seedling Vigor. The score is based on the speed of emergence ofthe plants within a plot relative to other plots within an experiment. Ascore of 9 indicates that 90% of plants growing have expanded firstleaves. A score of 1 indicates no plants have expanded first leaves.

SDS=Sudden Death Syndrome. Tolerance to Sudden Death Syndrome is ratedon a scale of 1 to 9, with a score of 1 being very susceptible rangingup to a score of 9 being tolerant.

S/LB=Seeds per Pound. Soybean seeds vary in seed size, therefore, thenumber of seeds required to make up one pound also varies. This affectsthe pounds of seed required to plant a given area, and can also impactend uses.

SHATTR=Shattering. This refers to the amount of pod dehiscence prior toharvest. Pod dehiscence involves seeds falling from the pods to thesoil. This is a visual score from 1 to 9 comparing all genotypes withina given test. A score of 9 means pods have not opened and no seeds havefallen out. A score of 5 indicates approximately 50% of the pods haveopened, with seeds falling to the ground and a score of 1 indicates 100%of the pods are opened.

SHOOTS. These are a portion of the body of the plant. They consist ofstems, petioles and leaves.

STC=Stearic Acid Percent. Stearic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

WH MD=White Mold Tolerance. This is a visual disease score from 1 to 9comparing all genotypes in a given test. The score is based uponobservations of mycelial growth and death of plants. A score of 9indicates no symptoms. Visual scores of 1 indicate complete death of theexperimental unit.

Definitions for Area of Adaptability

When referring to area of adaptability, such term is used to describethe location with the environmental conditions that would be well suitedfor this soybean variety. Area of adaptability is based on a number offactors, for example: days to maturity, insect resistance, diseaseresistance, and drought resistance. Area of adaptability does notindicate that the soybean variety will grow in every location within thearea of adaptability or that it will not grow outside the area. Area ofadaptability may also be used to refer to the soil or growingconditions.

-   Midwest: Iowa and Missouri-   Heartland: Illinois and the western half of Indiana-   Plains: ⅔ of the eastern parts of South Dakota and Nebraska-   North Central: Minnesota, Wisconsin, the Upper Peninsula of    Michigan, and the eastern half of North Dakota-   Mideast: Michigan, Ohio, and the eastern half of Indiana-   Eastern: Pennsylvania, Delaware, Maryland, Rhode Island, New Jersey,    Connecticut, Massachusetts, New York, Vermont, and Maine-   Southern: Virginia, West Virginia, Tennessee, Kentucky, Arkansas,    North Carolina, South Carolina, Georgia, Florida, Alabama,    Mississippi, and Louisiana-   Western: Texas, Kansas, Colorado, Oklahoma, New Mexico, Arizona,    Utah, Nevada, California, Washington, Oregon, Montana, Idaho,    Wyoming, the western half of North Dakota, and the western ⅓ South    Dakota and Nebraska-   PMG infested soils: soils containing Phytophthora sojae-   Narrow rows: 7″ and 15″ row spacing-   High yield environments: areas which lack normal stress for example    they have sufficient rainfall, water drainage, low disease pressure,    and low weed pressure-   Tough environments: areas which have stress challenges, opposite of    a high yield environment-   SCN infected soils: soils containing soybean cyst nematode other    areas of adaptation include the soybean growing regions of Canada,    tight clay soils, light sandy soils and no-till locations.

DETAILED DESCRIPTION OF INVENTION

The variety of the invention has shown uniformity and stability for alltraits, as described in the following variety description information.It has been self-pollinated a sufficient number of generations, withcareful attention to uniformity of plant type to ensure a sufficientlevel of homozygosity and phenotypic stability. The variety has beenincreased with continued observation for uniformity. No variant traitshave been observed or are expected.

Soybean variety XB39N05 is particularly adapted to the Midwest, Mideast,Southern, Western, Heartland and Eastern United States.

Soybean variety XB39N05 demonstrates a valuable combination of traits,including exceptional yield potential, resistance to glyphosate,Phytophthora resistance provided by the Rps1k gene, resistance to Race 3Soybean cyst nematode, and excellent Brown stem rot tolerance. There arefew other varieties at this RM which have the yield potential,multi-race phytophthora resistance as governed by the Rps1k gene,resistance to Race 3 Soybean cyst nematode, Brown stem rot tolerance,and resistance to glyphosate as exhibited by XB39N05.

Soybean variety XB39N05 exhibits a relative maturity of 3 and a subgroupof approximately 9. A variety description of Soybean variety XB39N05 isprovided in Table 1. Traits reported are average values for alllocations and years or samples measured.

Soybean variety XB39N05, being substantially homozygous, can bereproduced by planting seeds of the variety, growing the resultingsoybean plants under self-pollinating or sib-pollinating conditions, andharvesting the resulting seed, using techniques familiar to theagricultural arts.

Performance Examples of XB39N05

In the examples in Table 2, the traits and characteristics of soybeanvariety XB39N05 are given in paired comparisons with the Pioneervarieties shown in the following tables. Traits reported are mean valuesfor all locations and years where paired comparison data was obtained.

Further Embodiments of the Invention

Genetic Marker Profile through SSR and First Generation Progeny

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety or be used to determine or validate a pedigree.Genetic marker profiles can be obtained by techniques such asRestriction Fragment Length Polymorphisms (RFLPs), Randomly AmplifiedPolymorphic DNAs (RAPDs), Arbitrarily Primed Polymerase Chain Reaction(AP-PCR), DNA Amplification Fingerprinting (DAF), Sequence CharacterizedAmplified Regions (SCARs), Amplified Fragment Length Polymorphisms(AFLPs), Simple Sequence Repeats (SSRs) which are also referred to asMicrosatellites, and Single Nucleotide Polymorphisms (SNPs). Forexample, see Cregan et. al, “An Integrated Genetic Linkage Map of theSoybean Genome” Crop Science 39:1464–1490 (1999), and Berry et al.,Assessing Probability of Ancestry Using Simple Sequence Repeat Profiles:Applications to Maize Inbred Lines and Soybean Varieties” Genetics165:331–342 (2003), each of which are incorporated by reference hereinin their entirety.

Particular markers used for these purposes are not limited to anyparticular set of markers, but are envisioned to include any type ofmarker and marker profile which provides a means of distinguishingvarieties. One method of comparison is to use only homozygous loci forXB39N05. For example, one set of publicly available markers which couldbe used to screen and identify variety XB39N05 is disclosed in Table 3.

Primers and PCR protocols for assaying these and other markers aredisclosed in the Soybase (sponsored by the USDA Agricultural ResearchService and Iowa State University) located at the world wide web at129.186.26.94/SSR.html. In addition to being used for identification ofsoybean variety XB39N05 and plant parts and plant cells of varietyXB39N05, the genetic profile may be used to identify a soybean plantproduced through the use of XB39N05 or to verify a pedigree for progenyplants produced through the use of XB39N05. The genetic marker profileis also useful in breeding and developing backcross conversions.

The present invention comprises a soybean plant characterized bymolecular and physiological data obtained from the representative sampleof said variety deposited with the ATCC. Further provided by theinvention is a soybean plant formed by the combination of the disclosedsoybean plant or plant cell with another soybean plant or cell andcomprising the homozygous alleles of the variety.

Means of performing genetic marker profiles using SSR polymorphisms arewell known in the art. SSRs are genetic markers based on polymorphismsin repeated nucleotide sequences, such as microsatellites. A markersystem based on SSRs can be highly informative in linkage analysisrelative to other marker systems in that multiple alleles may bepresent. Another advantage of this type of marker is that, through useof flanking primers, detection of SSRs can be achieved, for example, bythe polymerase chain reaction (PCR), thereby eliminating the need forlabor-intensive Southern hybridization. The PCR detection is done by useof two oligonucleotide primers flanking the polymorphic segment ofrepetitive DNA. Repeated cycles of heat denaturation of the DNA followedby annealing of the primers to their complementary sequences at lowtemperatures, and extension of the annealed primers with DNA polymerase,comprise the major part of the methodology.

Following amplification, markers can be scored by electrophoresis of theamplification products. Scoring of marker genotype is based on the sizeof the amplified fragment, which may be measured by base pair weight ormolecular weight of the fragment. While variation in the primer used orin laboratory procedures can affect the reported fragment size, relativevalues should remain constant regardless of the specific primer orlaboratory used. When comparing varieties it is preferable if all SSRprofiles are performed in the same lab.

Primers used are publicly available and may be found in the Soybase orCregan supra. See also, PCT Publication No. WO 99/31964 NucleotidePolymorphisms in Soybean, U.S. Pat. No. 6,162,967 Positional Cloning ofSoybean Cyst Nematode Resistance Genes, and US2002/0129402A1 SoybeanSudden Death Syndrome Resistant Soybeans and Methods of Breeding andIdentifying Resistant Plants, the disclosure of which are incorporatedherein by reference.

The SSR profile of soybean plant XB39N05 can be used to identify plantscomprising XB39N05 as a parent, since such plants will comprise the samehomozygous alleles as XB39N05. Because the soybean variety isessentially homozygous at all relevant loci, most loci should have onlyone type of allele present. In contrast, a genetic marker profile of anF1 progeny should be the sum of those parents, e.g., if one parent washomozygous for allele x at a particular locus, and the other parenthomozygous for allele y at that locus, then the F1 progeny will be xy(heterozygous) at that locus. Subsequent generations of progeny producedby selection and breeding are expected to be of genotype x (homozygous),y (homozygous), or xy (heterozygous) for that locus position. When theF1 plant is selfed or sibbed for successive filial generations, thelocus should be either x or y for that position.

In addition, plants and plant parts substantially benefiting from theuse of XB39N05 in their development, such as XB39N05 comprising abackcross conversion, transgene, or genetic sterility factor, may beidentified by having a molecular marker profile with a high percentidentity to XB39N05. Such a percent identity might be 95%, 96%, 97%,98%, 99%, 99.5% or 99.9% identical to XB39N05.

The SSR profile of XB39N05 also can be used to identify essentiallyderived varieties and other progeny varieties developed from the use ofXB39N05, as well as cells and other plant parts thereof. Such plants maybe developed using the markers identified in WO 00/31964, U.S. Pat. No.6,162,967 and US2002/0129402A1. Progeny plants and plant parts producedusing XB39N05 may be identified by having a molecular marker profile ofat least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 76%,77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5% geneticcontribution from soybean variety, as measured by either percentidentity or percent similarity. Such progeny may be furthercharacterized as being within a pedigree distance of XB39N05, such aswithin 1,2,3, 4 or 5 or less cross-pollinations to a soybean plant otherthan XB39N05 or a plant that has XB39N05 as a progenitor. Uniquemolecular profiles may be identified with other molecular tools such asSNPs and RFLPs.

While determining the SSR genetic marker profile of the plants describedsupra, several unique SSR profiles may also be identified which did notappear in either parent of such plant. Such unique SSR profiles mayarise during the breeding process from recombination or mutation. Acombination of several unique alleles provides a means of identifying aplant variety, an F1 progeny produced from such variety, and progenyproduced from such variety.

Introduction of a New Trait or Locus into XB39N05

Variety XB39N05 represents a new base genetic variety into which a newlocus or trait may be introgressed. Direct transformation andbackcrossing represent two important methods that can be used toaccomplish such an introgression. The term backcross conversion andsingle locus conversion are used interchangeably to designate theproduct of a backcrossing program.

Backcross Conversions of XB39N05

A backcross conversion of XB39N05 occurs when DNA sequences areintroduced through backcrossing (Hallauer et al, 1988), with XB39N05utilized as the recurrent parent. Both naturally occurring andtransgenic DNA sequences may be introduced through backcrossingtechniques. A backcross conversion may produce a plant with a trait orlocus conversion in at least two or more backcrosses, including at least2 crosses, at least 3 crosses, at least 4 crosses, at least 5 crossesand the like. Molecular marker assisted breeding or selection may beutilized to reduce the number of backcrosses necessary to achieve thebackcross conversion. For example, see Openshaw, S. J. et al.,Marker-assisted Selection in Backcross Breeding. In: ProceedingsSymposium of the Analysis of Molecular Data, August 1994, Crop ScienceSociety of America, Corvallis, Oreg., where it is demonstrated that abackcross conversion can be made in as few as two backcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (single genes or closely linked genes as vs.unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear) and the types of parents includedin the cross. It is understood by those of ordinary skill in the artthat for single gene traits that are relatively easy to classify, thebackcross method is effective and relatively easy to manage. (SeeHallauer et al. in Corn and Corn Improvement, Sprague and Dudley, ThirdEd. 1998). Desired traits that may be transferred through backcrossconversion include, but are not limited to, sterility (nuclear andcytoplasmic), fertility restoration, nutritional enhancements, droughttolerance, nitrogen utilization, altered fatty acid profile, lowphytate, industrial enhancements, disease resistance (bacterial, fungalor viral), insect resistance and herbicide resistance. In addition, anintrogression site itself, such as an FRT site, Lox site or other sitespecific integration site, may be inserted by backcrossing and utilizedfor direct insertion of one or more genes of interest into a specificplant variety. In some embodiments of the invention, the number of locithat may be backcrossed into XB39N05 is at least 1, 2, 3, 4, or 5 and/orno more than 6, 5, 4, 3, or 2. A single locus may contain severaltransgenes, such as a transgene for disease resistance that, in the sameexpression vector, also contains a transgene for herbicide resistance.The gene for herbicide resistance may be used as a selectable markerand/or as a phenotypic trait. A single locus conversion of site specificintegration system allows for the integration of multiple genes at theconverted loci.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest is accomplished by direct selection for a traitassociated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the gene(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withselection for the converted trait.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are automaticallyrecovered after successive backcrosses. Poehlman, Breeding Field Crops,P. 204 (1987). Poehlman suggests from one to four or more backcrosses,but as noted above, the number of backcrosses necessary can be reducedwith the use of molecular markers. Other factors, such as a geneticallysimilar donor parent, may also reduce the number of backcrossesnecessary. As noted by Poehlman, backcrossing is easiest for simplyinherited, dominant and easily recognized traits.

One process for adding or modifying a trait or locus in soybean varietyXB39N05 comprises crossing XB39N05 plants grown from XB39N05 seed withplants of another soybean variety that comprise the desired trait orlocus, selecting F1 progeny plants that comprise the desired trait orlocus to produce selected F1 progeny plants, crossing the selectedprogeny plants with the XB39N05 plants to produce backcross progenyplants, selecting for backcross progeny plants that have the desiredtrait or locus and the morphological characteristics of soybean varietyXB39N05 to produce selected backcross progeny plants; and backcrossingto XB39N05 three or more times in succession to produce selected fourthor higher backcross progeny plants that comprise said trait or locus.The modified XB39N5 may be further characterized as having thephysiological and morphological characteristics of soybean varietyXB39N05 listed in Table 1 as determined at the 5% significance levelwhen grown in the same environmental conditions and/or may becharacterized by percent similarity or identity to XB39N05 as determinedby SSR markers. The above method may be utilized with fewer backcrossesin appropriate situations, such as when the donor parent is highlyrelated or markers are used in the selection step. Desired traits thatmay be used include those nucleic acids known in the art, some of whichare listed herein, that will affect traits through nucleic acidexpression or inhibition. Desired loci include the introgression of FRT,Lox and other sites for site specific integration, which may also affecta desired trait if a functional nucleic acid is inserted at theintegration site.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny soybean seed byadding a step at the end of the process that comprises crossing XB39N05with the introgressed trait or locus with a different soybean plant andharvesting the resultant first generation progeny soybean seed.

Transformation

The advent of new molecular biological techniques has allowed theisolation and characterization of genetic elements with specificfunctions, such as encoding specific protein products. Scientists in thefield of plant biology developed a strong interest in engineering thegenome of plants to contain and express foreign genetic elements, oradditional, or modified versions of native or endogenous geneticelements in order to alter the traits of a plant in a specific manner.Any DNA sequences, whether from a different species or from the samespecies, which are inserted into the genome using transformation arereferred to herein collectively as “transgenes”. In some embodiments ofthe invention, a transformed variant of XB39N05 may contain at least onetransgene but could contain at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10and/or no more than 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2.Over the last fifteen to twenty years several methods for producingtransgenic plants have been developed, and the present invention alsorelates to transformed versions of the claimed soybean variety XB39N05.

One embodiment of the invention is a process for producing soybeanvariety XB39N05 further comprising a desired trait, said processcomprising transforming a soybean plant of variety XB39N05 with atransgene that confers a desired trait. Another embodiment is theproduct produced by this process. In one embodiment the desired traitmay be one or more of herbicide resistance, insect resistance, diseaseresistance, decreased phytate, or modified fatty acid or carbohydratemetabolism. The specific gene may be any known in the art or listedherein, including; a polynucleotide conferring resistance toimidazolinone, sulfonylurea, glyphosate, glufosinate, triazine andbenzonitrile; a polynucleotide encoding a bacillus thuringiensispolypeptide, a polynucleotide encoding phytase, FAD-2, FAD-3, galactinolsynthase or a raffinose synthetic enzyme; or a polynucleotide conferringresistance to soybean cyst nematode, brown stem rot, phytophthora rootrot, soybean mosaic virus or sudden death syndrome.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67–88 and Armstrong, “The First Decade of Maize Transformation: A Reviewand Future Perspective” (Maydica 44:101–109, 1999). In addition,expression vectors and in vitro culture methods for plant cell or tissuetransformation and regeneration of plants are available. See, forexample, Gruber et al., “Vectors for Plant Transformation” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages 89–119.

The most prevalent types of plant transformation involve theconstruction of an expression vector. Such a vector comprises a DNAsequence that contains a gene under the control of or operatively linkedto a regulatory element, for example a promoter. The vector may containone or more genes and one or more regulatory elements.

A genetic trait which has been engineered into the genome of aparticular soybean plant using transformation techniques, could be movedinto the genome of another variety using traditional breeding techniquesthat are well known in the plant breeding arts. For example, abackcrossing approach is commonly used to move a transgene from atransformed soybean variety into an already developed soybean variety,and the resulting backcross conversion plant would then comprise thetransgene(s).

Various genetic elements can be introduced into the plant genome usingtransformation. These elements include, but are not limited to genes;coding sequences; inducible, constitutive, and tissue specificpromoters; enhancing sequences; and signal and targeting sequences. Forexample, see the traits, genes and transformation methods listed in U.S.Pat. No. 6,118,055.

With transgenic plants according to the present invention, a foreignprotein can be produced in commercial quantities. Thus, techniques forthe selection and propagation of transformed plants, which are wellunderstood in the art, yield a plurality of transgenic plants that areharvested in a conventional manner, and a foreign protein then can beextracted from a tissue of interest or from total biomass. Proteinextraction from plant biomass can be accomplished by known methods whichare discussed, for example, by Heney and Orr, Anal. Biochem. 114: 92–6(1981).

A genetic map can be generated, primarily via conventional RestrictionFragment Length Polymorphisms (RFLP), Polymerase Chain Reaction (PCR)analysis, Simple Sequence Repeats (SSR) and Single NucleotidePolymorphisms (SNP) that identifies the approximate chromosomal locationof the integrated DNA molecule. For exemplary methodologies in thisregard, see Glick and Thompson, METHODS IN PLANT MOLECULAR BIOLOGY ANDBIOTECHNOLOGY 269–284 (CRC Press, Boca Raton, 1993).

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science,280:1077–1082, 1998, and similar capabilities are becoming increasinglyavailable for the soybean genome. Map information concerning chromosomallocation is useful for proprietary protection of a subject transgenicplant. If unauthorized propagation is undertaken and crosses made withother germplasm, the map of the integration region can be compared tosimilar maps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons would involvehybridizations, RFLP, PCR, SSR and sequencing, all of which areconventional techniques. SNPs may also be used alone or in combinationwith other techniques.

Likewise, by means of the present invention, plants can be geneticallyengineered to express various phenotypes of agronomic interest. Throughthe transformation of soybean the expression of genes can be altered toenhance disease resistance, insect resistance, herbicide resistance,agronomic, grain quality and other traits. Transformation can also beused to insert DNA sequences which control or help controlmale-sterility. DNA sequences native to soybean as well as non-nativeDNA sequences can be transformed into soybean and used to alter levelsof native or non-native proteins. Various promoters, targetingsequences, enhancing sequences, and other DNA sequences can be insertedinto the genome for the purpose of altering the expression of proteins.Reduction of the activity of specific genes (also known as genesilencing, or gene suppression) is desirable for several aspects ofgenetic engineering in plants.

Many techniques for gene silencing are well known to one of skill in theart, including but not limited to knock-outs (such as by insertion of atransposable element such as mu (Vicki Chandler, The Maize Handbook ch.118 (Springer-Verlag 1994) or other genetic elements such as a FRT, Loxor other site specific integration site, antisense technology (see,e.g., Sheehy et al. (1988) PNAS USA 85:8805–8809; and U.S. Pat. Nos.5,107,065; 5,453, 566; and 5,759,829); co-suppression (e.g., Taylor(1997) Plant Cell 9:1245; Jorgensen (1990) Trends Biotech.8(12):340–344; Flavell (1994) PNAS USA 91:3490–3496; Finnegan et al.(1994) Bio/Technology 12: 883–888; and Neuhuber et al. (1994) Mol. Gen.Genet. 244:230–241); RNA interference (Napoli et al. (1990) Plant Cell2:279–289; U.S. Pat. No. 5,034,323; Sharp (1999) Genes Dev. 13:139–141;Zamore et al. (2000) Cell 101:25–33; and Montgomery et al. (1998) PNASUSA 95:15502–15507), virus-induced gene silencing (Burton, et al. (2000)Plant Cell 12:691–705; and Baulcombe (1999) Curr. Op. Plant Bio.2:109–113); target-RNA-specific ribozymes (Haseloff et al. (1988) Nature334: 585–591); hairpin structures (Smith et al. (2000) Nature407:319–320; WO 99/53050; and WO 98/53083); MicroRNA (Aukerman & Sakai(2003) Plant Cell 15:2730–2741); ribozymes (Steinecke et al. (1992) EMBOJ. 11:1525; and Perriman et al. (1993) Antisense Res. Dev. 3:253);oligonucleotide mediated targeted modification (e.g., WO 03/076574 andWO 99/25853); Zn-finger targeted molecules (e.g., WO 01/52620; WO03/048345; and WO 00/42219); and other methods or combinations of theabove methods known to those of skill in the art.

Exemplary nucleotide sequences that may be altered by geneticengineering include, but are not limited to, those categorized below.

1. Transgenes that Confer Resistance to Insects or Disease and thatEncode:

(A) Plant disease resistance genes. Plant defenses are often activatedby specific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant variety can be transformed with clonedresistance gene to engineer plants that are resistant to specificpathogen strains. See, for example Jones et al., Science 266: 789 (1994)(cloning of the tomato Cf-9 gene for resistance to Cladosporium fulvum);Martin et al., Science 262: 1432 (1993) (tomato Pto gene for resistanceto Pseudomonas syringae pv. tomato encodes a protein kinase); Mindrinoset al., Cell 78: 1089 (1994) (Arabidopsis RSP2 gene for resistance toPseudomonas syringae), McDowell & Woffenden, (2003) Trends Biotechnol.21(4):178–83 and Toyoda et al., (2002) Transgenic Res. 11 (6):567–82. Aplant resistant to a disease is one that is more resistant to a pathogenas compared to the wild type plant.

(B) A Bacillus thuringiensis protein, a derivative thereof or asynthetic polypeptide modeled thereon. See, for example, Geiser et al.,Gene 48: 109 (1986), who disclose the cloning and nucleotide sequence ofa Bt delta-endotoxin gene. Moreover, DNA molecules encodingdelta-endotoxin genes can be purchased from American Type CultureCollection (Rockville, Md.), for example, under ATCC Accession Nos.40098, 67136, 31995 and 31998. Other examples of Bacillus thuringiensistransgenes being genetically engineered are given in the followingpatents and patent applications and hereby are incorporated by referencefor this purpose: U.S. Pat. Nos. 5,188,960; 5,689,052; 5,880,275; WO91/14778; WO 99/31248; WO 01/12731; WO 99/24581; WO 97/40162 and U.S.application Ser. Nos. 10/032,717; 10/414,637; and 10/606,320.

(C) An insect-specific hormone or pheromone such as an ecdysteroid andjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. See, for example, the disclosure byHammock et al., Nature 344: 458 (1990), of baculovirus expression ofcloned juvenile hormone esterase, an inactivator of juvenile hormone.

(D) An insect-specific peptide which, upon expression, disrupts thephysiology of the affected pest. For example, see the disclosures ofRegan, J. Biol. Chem. 269: 9 (1994) (expression cloning yields DNAcoding for insect diuretic hormone receptor); Pratt et al., Biochem.Biophys. Res. Comm. 163: 1243 (1989) (an allostatin is identified inDiploptera puntata); Chattopadhyay et al. (2004) Critical Reviews inMicrobiology 30 (1): 33–54 2004; Zjawiony (2004) J Nat Prod 67 (2):300–310; Carlini & Grossi-de-Sa (2002) Toxicon, 40 (11): 1515–1539;Ussuf et al. (2001) Curr Sci. 80 (7): 847–853; and Vasconcelos &Oliveira (2004) Toxicon 44 (4): 385–403. See also U.S. Pat. No.5,266,317 to Tomalski et al., who disclose genes encodinginsect-specific toxins.

(E) An enzyme responsible for a hyperaccumulation of a monterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivativeor another non-protein molecule with insecticidal activity.

(F) An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See PCTapplication WO 93/02197 in the name of Scott et al., which discloses thenucleotide sequence of a callase gene. DNA molecules which containchitinase-encoding sequences can be obtained, for example, from the ATCCunder Accession Nos. 39637 and 67152. See also Kramer et al., InsectBiochem. Molec. Biol. 23: 691 (1993), who teach the nucleotide sequenceof a cDNA encoding tobacco hookworm chitinase, and Kawalleck et al.,Plant Molec. Biol. 21: 673 (1993), who provide the nucleotide sequenceof the parsley ubi4-2 polyubiquitin gene, U.S. application Ser. Nos.10/389,432, 10/692,367, and U.S. Pat. No. 6,563,020.

(G) A molecule that stimulates signal transduction. For example, see thedisclosure by Botella et al., Plant Molec. Biol. 24: 757 (1994), ofnucleotide sequences for mung bean calmodulin cDNA clones, and Griess etal., Plant Physiol. 104: 1467 (1994), who provide the nucleotidesequence of a maize calmodulin cDNA clone.

(H) A hydrophobic moment peptide. See PCT application WO 95/16776 andU.S. Pat. No. 5,580,852 disclosure of peptide derivatives of Tachyplesinwhich inhibit fungal plant pathogens) and PCT application WO 95/18855and U.S. Pat. No. 5,607,914 (teaches synthetic antimicrobial peptidesthat confer disease resistance).

(I) A membrane permease, a channel former or a channel blocker. Forexample, see the disclosure by Jaynes et al., Plant Sci. 89: 43 (1993),of heterologous expression of a cecropin-beta lytic peptide analog torender transgenic tobacco plants resistant to Pseudomonas solanacearum.

(J) A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses. See Beachy et al., Ann. Rev. Phytopathol.28: 451 (1990). Coat protein-mediated resistance has been conferred upontransformed plants against alfalfa mosaic virus, cucumber mosaic virus,tobacco streak virus, potato virus X, potato virus Y, tobacco etchvirus, tobacco rattle virus and tobacco mosaic virus. Id.

(K) An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect. Cf.Taylor et al., Abstract #497, SEVENTH INT'L SYMPOSIUM ON MOLECULARPLANT-MICROBE INTERACTIONS (Edinburgh, Scotland, 1994) (enzymaticinactivation in transgenic tobacco via production of single-chainantibody fragments).

(L) A virus-specific antibody. See, for example, Tavladoraki et al.,Nature 366: 469 (1993), who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

(M) A developmental-arrestive protein produced in nature by a pathogenor a parasite. Thus, fungal endo alpha-1,4-D-polygalacturonasesfacilitate fungal colonization and plant nutrient release bysolubilizing plant cell wall homo-alpha-1,4-D-galacturonase. See Lamb etal., Bio/Technology 10: 1436 (1992). The cloning and characterization ofa gene which encodes a bean endopolygalacturonase-inhibiting protein isdescribed by Toubart et al., Plant J. 2: 367 (1992).

(N) A developmental-arrestive protein produced in nature by a plant. Forexample, Logemann et al., Bio/Technology 10: 305 (1992), have shown thattransgenic plants expressing the barley ribosome-inactivating gene havean increased resistance to fungal disease.

(O) Genes involved in the Systemic Acquired Resistance (SAR) Responseand/or the pathogenesis related genes. Briggs, S., Current Biology, 5(2)(1995), Pieterse & Van Loon (2004) Curr. Opin. Plant Bio. 7(4):456–64and Somssich (2003) Cell 113(7):815–6.

(P) Antifungal genes (Cornelissen and Melchers, Pl. Physiol.101:709–712, (1993) and Parijs et al., Planta 183:258–264, (1991) andBushnell et al., Can. J. of Plant Path. 20(2):137–149 (1998). Also seeU.S. application Ser. No. 09/950,933.

(Q) Detoxification genes, such as for fumonisin, beauvericin,moniliformin and zearalenone and their structurally related derivatives.For example, see U.S. Pat. No. 5,792,931.

(R) Cystatin and cysteine proteinase inhibitors. See U.S. applicationSer. No. 10/947,979.

(S) Defensin genes. See WO03000863 and U.S. application Ser. No.10/178,213.

(T) Genes conferring resistance to nematodes, and in particular soybeancyst nematodes. See e.g. PCT Application WO96/30517; PCT ApplicationWO93/19181, WO 03/033651 and Urwin et al., Planta 204:472–479 (1998),Williamson (1999) Curr Opin Plant Bio. 2(4):327–31.

(U) Genes that confer resistance to Phytophthora Root Rot, such as theRps 1, Rps 1-a, Rps 1-b, Rps 1-c, Rps 1-d, Rps 1-e, Rps 1-k, Rps 2, Rps3-a, Rps 3-b, Rps 3-c, Rps 4, Rps 5, Rps 6, Rps 7 and other Rps genes.See, for example, Shoemaker et al, Phytophthora Root Rot Resistance GeneMapping in Soybean, Plant Genome IV Conference, San Diego, Calif.(1995).

(V) Genes that confer resistance to Brown Stem Rot, such as described inU.S. Pat. No. 5,689,035 and incorporated by reference for this purpose.

2. Transgenes that Confer Resistance to a Herbicide, for Example:

(A) A herbicide that inhibits the growing point or meristem, such as animidazolinone or a sulfonylurea. Exemplary genes in this category codefor mutant ALS and AHAS enzyme as described, for example, by Lee et al.,EMBO J. 7: 1241 (1988), and Miki et al., Theor. Appl. Genet. 80: 449(1990), respectively. See also, U.S. Pat. Nos. 5,605,011; 5,013,659;5,141,870; 5,767,361; 5,731,180; 5,304,732; 4,761,373; 5,331,107;5,928,937; and 5,378,824; and international publication WO 96/33270,which are incorporated herein by reference for this purpose.

(B) Glyphosate (resistance imparted by mutant5-enolpyruvl-3-phosphikimate synthase (EPSP) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus phosphinothricin acetyl transferase (bar) genes), andpyridinoxy or phenoxy proprionic acids and cycloshexones (ACCaseinhibitor-encoding genes). See, for example, U.S. Pat. No. 4,940,835 toShah et al., which discloses the nucleotide sequence of a form of EPSPSwhich can confer glyphosate resistance. U.S. Pat. No. 5,627,061 to Barryet al. also describes genes encoding EPSPS enzymes. See also U.S. Pat.Nos. 6,566,587; 6,338,961; 6,248,876 B1; 6,040,497; 5,804,425;5,633,435; 5,145,783; 4,971,908; 5,312,910; 5,188,642; 4,940,835;5,866,775; 6,225,114 B1; 6,130,366; 5,310,667; 4,535,060; 4,769,061;5,633,448; 5,510,471; Re. 36,449; RE 37,287 E; and 5,491,288; andinternational publications EP1173580; WO 01/66704; EP1173581 andEP1173582, which are incorporated herein by reference for this purpose.Glyphosate resistance is also imparted to plants that express a genethat encodes a glyphosate oxido-reductase enzyme as described more fullyin U.S. Pat. Nos. 5,776,760 and 5,463,175, which are incorporated hereinby reference for this purpose. In addition glyphosate resistance can beimparted to plants by the over expression of genes encoding glyphosateN-acetyltransferase. See, for example, U.S. Application Serial Nos.US01/46227; Ser. Nos. 10/427,692 and 10/427,692. A DNA molecule encodinga mutant aroA gene can be obtained under ATCC accession No. 39256, andthe nucleotide sequence of the mutant gene is disclosed in U.S. Pat. No.4,769,061 to Comai. European Patent Application No. 0 333 033 to Kumadaet al. and U.S. Pat. No. 4,975,374 to Goodman et al. disclose nucleotidesequences of glutamine synthetase genes which confer resistance toherbicides such as L-phosphinothricin. The nucleotide sequence of aphosphinothricin-acetyl-transferase gene is provided in European PatentNo. 0 242 246 and 0 242 236 to Leemans et al. De Greef et al.,Bio/Technology 7: 61 (1989), describe the production of transgenicplants that express chimeric bar genes coding for phosphinothricinacetyl transferase activity. See also, U.S. Pat. Nos. 5,969,213;5,489,520; 5,550,318; 5,874,265; 5,919,675; 5,561,236; 5,648,477;5,646,024; 6,177,616 B1; and 5,879,903, which are incorporated herein byreference for this purpose. Exemplary genes conferring resistance tophenoxy proprionic acids and cycloshexones, such as sethoxydim andhaloxyfop, are the Acc1-S1, Acc1-S2 and Acc1-S3 genes described byMarshall et al., Theor. Appl. Genet. 83: 435 (1992).

(C) A herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al.,Plant Cell 3: 169 (1991), describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648 to Stalker, andDNA molecules containing these genes are available under ATCC AccessionNos. 53435, 67441 and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al., Biochem. J. 285:173 (1992).

(D) Acetohydroxy acid synthase, which has been found to make plants thatexpress this enzyme resistant to multiple types of herbicides, has beenintroduced into a variety of plants (see, e.g., Hattori et al. (1995)Mol Gen Genet 246:419). Other genes that confer resistance to herbicidesinclude: a gene encoding a chimeric protein of rat cytochrome P4507A1and yeast NADPH-cytochrome P450 oxidoreductase (Shiota et al. (1994)Plant Physiol 106:17), genes for glutathione reductase and superoxidedismutase (Aono et al. (1995) Plant Cell Physiol 36:1687, and genes forvarious phosphotransferases (Datta et al. (1992) Plant Mol Biol 20:619).

(E) Protoporphyrinogen oxidase (protox) is necessary for the productionof chlorophyll, which is necessary for all plant survival. The protoxenzyme serves as the target for a variety of herbicidal compounds. Theseherbicides also inhibit growth of all the different species of plantspresent, causing their total destruction. The development of plantscontaining altered protox activity which are resistant to theseherbicides are described in U.S. Pat. Nos. 6,288,306 B1; 6,282,837 B1;and 5,767,373; and international publication WO 01/12825.

3. Transgenes that Confer or Contribute to an Altered GrainCharacteristic, such as:

-   -   (A) Altered fatty acids, for example, by        -   (1) Down-regulation of stearoyl-ACP desaturase to increase            stearic acid content of the plant. See Knultzon et al.,            Proc. Natl. Acad. Sci. USA 89: 2624 (1992) and WO99/64579            (Genes for Desaturases to Alter Lipid Profiles in Corn),        -   (2) Elevating oleic acid via FAD-2 gene modification and/or            decreasing linolenic acid via FAD-3 gene modification (see            U.S. Pat. Nos. 6,063,947; 6,323,392; 6,372,965 and WO            93/11245),        -   (3) Altering conjugated linolenic or linoleic acid content,            such as in WO 01/12800,        -   (4) Altering LEC1, AGP, Dek1, Superal1, mi1ps, various Ipa            genes such as Ipa1, Ipa3, hpt or hggt. For example, see WO            02/42424, WO 98/22604, WO 03/011015, U.S. Pat. No.            6,423,886, U.S. Pat. No. 6,197,561, U.S. Pat. No. 6,825,397,            US2003/0079247, US2003/0204870, WO02/057439, WO03/011015 and            Rivera-Madrid, R. et al. Proc. Natl. Acad. Sci. 92:5620–5624            (1995).    -   (B) Altered phosphorus content, for example, by the        -   (1) Introduction of a phytase-encoding gene would enhance            breakdown of phytate, adding more free phosphate to the            transformed plant. For example, see Van Hartingsveldt et            al., Gene 127: 87 (1993), for a disclosure of the nucleotide            sequence of an Aspergillus niger phytase gene.        -   (2) Up-regulation of a gene that reduces phytate content. In            maize, this, for example, could be accomplished, by cloning            and then re-introducing DNA associated with one or more of            the alleles, such as the LPA alleles, identified in maize            mutants characterized by low levels of phytic acid, such as            in Raboy et al., Maydica 35: 383 (1990) and/or by altering            inositol kinase activity as in WO 02/059324, US2003/0009011,            WO 03/027243, US2003/0079247, WO 99/05298, U.S. Pat. No.            6,197,561, U.S. Pat. No. 6,291,224, U.S. Pat. No. 6,391,348,            WO2002/059324, US2003/0079247, Wo98/45448, WO99/55882,            WO01/04147.    -   (C) Altered carbohydrates effected, for example, by altering a        gene for an enzyme that affects the branching pattern of starch,        a gene altering thioredoxin. (See U.S. Pat. No. 6,531,648). See        Shiroza et al., J. Bacteriol. 170: 810 (1988) (nucleotide        sequence of Streptococcus mutans fructosyltransferase gene),        Steinmetz et al., Mol. Gen. Genet. 200: 220 (1985) (nucleotide        sequence of Bacillus subtilis levansucrase gene), Pen et al.,        Bio/Technology 10: 292 (1992) (production of transgenic plants        that express Bacillus licheniformis alpha-amylase), Elliot et        al., Plant Molec. Biol. 21: 515 (1993) (nucleotide sequences of        tomato invertase genes), SOgaard et al., J. Biol. Chem. 268:        22480 (1993) (site-directed mutagenesis of barley alpha-amylase        gene), and Fisher et al., Plant Physiol. 102: 1045 (1993) (maize        endosperm starch branching enzyme II), WO 99/10498 (improved        digestibility and/or starch extraction through modification of        UDP-D-xylose 4-epimerase, Fragile 1 and 2, Ref1, HCHL, C4H),        U.S. Pat. No. 6,232,529 (method of producing high oil seed by        modification of starch levels (AGP)). The fatty acid        modification genes mentioned above may also be used to affect        starch content and/or composition through the interrelationship        of the starch and oil pathways.    -   (D) Altered antioxidant content or composition, such as        alteration of tocopherol or tocotrienols. For example, see U.S.        Pat. No. 6,787,683, US2004/0034886 and WO 00/68393 involving the        manipulation of antioxidant levels through alteration of a phytl        prenyl transferase (ppt), WO 03/082899 through alteration of a        homogentisate geranyl geranyl transferase (hggt).    -   (E) Altered essential seed amino acids. For example, see U.S.        Pat. No. 6,127,600 (method of increasing accumulation of        essential amino acids in seeds), U.S. Pat. No. 6,080,913 (binary        methods of increasing accumulation of essential amino acids in        seeds), U.S. Pat. No. 5,990,389 (high lysine), WO99/40209        (alteration of amino acid compositions in seeds), WO99/29882        (methods for altering amino acid content of proteins), U.S. Pat.        No. 5,850,016 (alteration of amino acid compositions in seeds),        WO98/20133 (proteins with enhanced levels of essential amino        acids), U.S. Pat. No. 5,885,802 (high methionine), U.S. Pat. No.        5,885,801 (high threonine), U.S. Pat. No. 6,664,445 (plant amino        acid biosynthetic enzymes), U.S. Pat. No. 6,459,019 (increased        lysine and threonine), U.S. Pat. No. 6,441,274 (plant tryptophan        synthase beta subunit), U.S. Pat. No. 6,346,403 (methionine        metabolic enzymes), U.S. Pat. No. 5,939,599 (high sulfur), U.S.        Pat. No. 5,912,414 (increased methionine), WO98/56935 (plant        amino acid biosynthetic enzymes), WO98/45458 (engineered seed        protein having higher percentage of essential amino acids),        WO98/42831 (increased lysine), U.S. Pat. No. 5,633,436        (increasing sulfur amino acid content), U.S. Pat. No. 5,559,223        (synthetic storage proteins with defined structure containing        programmable levels of essential amino acids for improvement of        the nutritional value of plants), WO96/01905 (increased        threonine), WO95/15392 (increased lysine), US2003/0163838,        US2003/0150014, US2004/0068767, U.S. Pat. No. 6,803,498,        WO01/79516, and WO00/09706 (Ces A: cellulose synthase), U.S.        Pat. No. 6,194,638 (hemicellulose), U.S. Pat. No. 6,399,859 and        US2004/0025203 (UDPGdH), U.S. Pat. No. 6,194,638 (RGP).        4. Genes that Control Male-Sterility

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al. and chromosomal translocations asdescribed by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al., U.S. Pat. No. 5,432,068,describe a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene that confers male fertilityto be transcribed.

(A) Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT (WO 01/29237).

(B) Introduction of various stamen-specific promoters (WO 92/13956, WO92/13957).

(C) Introduction of the barnase and the barstar gene (Paul et al. PlantMol. Biol. 19:611–622, 1992).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. No. 5,859,341; U.S. Pat. No. 6,297,426; U.S.Pat. No. 5,478,369; U.S. Pat. No. 5,824,524; U.S. Pat. No. 5,850,014;and U.S. Pat. No. 6,265,640; all of which are hereby incorporated byreference.

5. Genes that create a site for site specific DNA integration. Thisincludes the introduction of FRT sites that may be used in the FLP/FRTsystem and/or Lox sites that may be used in the Cre/Loxp system. Forexample, see Lyznik, et al., Site-Specific Recombination for GeneticEngineering in Plants, Plant Cell Rep (2003) 21:925–932 and WO 99/25821,which are hereby incorporated by reference. Other systems that may beused include the Gin recombinase of phage Mu (Maeser et al., 1991; VickiChandler, The Maize Handbook ch. 118 (Springer-Verlag 1994), the Pinrecombinase of E. coli (Enomoto et al., 1983), and the R/RS system ofthe pSR1 plasmid (Araki et al., 1992).

6. Genes that affect abiotic stress resistance (including but notlimited to flowering, ear and seed development, enhancement of nitrogenutilization efficiency, altered nitrogen responsiveness, droughtresistance or tolerance, cold resistance or tolerance, and saltresistance or tolerance) and increased yield under stress. For example,see: WO 00/73475 where water use efficiency is altered throughalteration of malate; U.S. Pat. No. 5,892,009, U.S. Pat. No. 5,965,705,U.S. Pat. No. 5,929,305, U.S. Pat. No. 5,891,859, U.S. Pat. No.6,417,428, U.S. Pat. No. 6,664,446, U.S. Pat. No. 6,706,866, U.S. Pat.No. 6,717,034, U.S. Pat. No. 6,801,104, WO2000060089, WO2001026459,WO2001035725, WO2001034726, WO2001035727, WO2001036444, WO2001036597,WO2001036598, WO2002015675, WO2002017430, WO2002077185, WO2002079403,WO2003013227, WO2003013228, WO2003014327, WO2004031349, WO2004076638,WO9809521, and WO9938977 describing genes, including CBF genes andtranscription factors effective in mitigating the negative effects offreezing, high salinity, and drought on plants, as well as conferringother positive effects on plant phenotype; US2004/0148654 and WO01/36596where abscisic acid is altered in plants resulting in improved plantphenotype such as increased yield and/or increased tolerance to abioticstress; WO2000/006341, WO04/090143, U.S. application Ser. Nos.10/817,483 and 09/545,334 where cytokinin expression is modifiedresulting in plants with increased stress tolerance, such as droughttolerance, and/or increased yield. Also see WO0202776, WO2003052063,JP2002281975, U.S. Pat. No. 6,084,153, WO0164898, U.S. Pat. No.6,177,275, and U.S. Pat. No. 6,107,547 (enhancement of nitrogenutilization and altered nitrogen responsiveness). For ethylenealteration, see US20040128719, US20030166197 and WO200032761. For planttranscription factors or transcriptjonal regulators of abiotic stress,see e.g. US20040098764 or US20040078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth and/or plantstructure, can be introduced or introgressed into plants, see e.g.WO97/49811 (LHY), WO98/56918 (ESD4), WO97/10339 and US6573430 (TFL),US6713663 (FT), WO96/14414 (CON), WO96/38560, WO01/21822 (VRN1),WO00/44918 (VRN2), WO99/49064 (GI), WO00/46358 (FRI), WO97/29123,US6794560, US6307126 (GAI), WO99/09174 (D8 and Rht), and WO2004076638and WO2004031349 (transcription factors).

Using XB39N05 to develop other soybean varieties

Soybean varieties such as XB39N05 are typically developed for use inseed and grain production. However, soybean varieties such as XB39N05also provide a source of breeding material that may be used to developnew soybean varieties. Plant breeding techniques known in the art andused in a soybean plant breeding program include, but are not limitedto, recurrent selection, mass selection, bulk selection, mass selection,backcrossing, pedigree breeding, open pollination breeding, restrictionfragment length polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of soybeanvarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits but genotypic analysis may also be used.

Using XB39N05 in a Breeding Program

This invention is directed to methods for producing a soybean plant bycrossing a first parent soybean plant with a second parent soybean plantwherein either the first or second parent soybean plant is varietyXB39N05. The other parent may be any other soybean plant, such as asoybean plant that is part of a synthetic or natural population. Anysuch methods using soybean variety XB39N05 are part of this invention:selfing, sibbing, backcrosses, mass selection, pedigree breeding, bulkselection, hybrid production, crosses to populations, and the like.These methods are well known in the art and some of the more commonlyused breeding methods are described below. Descriptions of breedingmethods can be found in one of several reference books (e.g., Allard,Principles of Plant Breeding, 1960; Simmonds, Principles of CropImprovement, 1979; Sneep et al., 1979; Fehr, “Breeding Methods forCultivar Development”, Chapter 7, Soybean Improvement, Production andUses, 2^(nd ed., Wilcox editor,) 1987).

Pedigree Breeding

Pedigree breeding starts with the crossing of two genotypes, such asXB39N05 and another soybean variety having one or more desirablecharacteristics that is lacking or which complements XB39N05. If the twooriginal parents do not provide all the desired characteristics, othersources can be included in the breeding population. In the pedigreemethod, superior plants are selfed and selected in successive filialgenerations. In the succeeding filial generations the heterozygouscondition gives way to homogeneous varieties as a result ofself-pollination and selection. Typically in the pedigree method ofbreeding, five or more successive filial generations of selfing andselection is practiced: F1→F2; F2→F3; F3→F4; F4→F₅, etc. After asufficient amount of inbreeding, successive filial generations willserve to increase seed of the developed variety. Preferably, thedeveloped variety comprises homozygous alleles at about 95% or more ofits loci.

In addition to being used to create a backcross conversion, backcrossingcan also be used in combination with pedigree breeding. As discussedpreviously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety, the donor parent, to adeveloped variety called the recurrent parent, which has overall goodagronomic characteristics yet lacks that desirable trait or traits.However, the same procedure can be used to move the progeny toward thegenotype of the recurrent parent but at the same time retain manycomponents of the non-recurrent parent by stopping the backcrossing atan early stage and proceeding with selfing and selection. For example, asoybean variety may be crossed with another variety to produce a firstgeneration progeny plant. The first generation progeny plant may then bebackcrossed to one of its parent varieties to create a BC1 or BC2.Progeny are selfed and selected so that the newly developed variety hasmany of the attributes of the recurrent parent and yet several of thedesired attributes of the non-recurrent parent. This approach leveragesthe value and strengths of the recurrent parent for use in new soybeanvarieties.

Therefore, an embodiment of this invention is a method of making abackcross conversion of soybean variety XB39N05, comprising the steps ofcrossing a plant of soybean variety XB39N05 with a donor plantcomprising a desired trait, selecting an F1 progeny plant comprising thedesired trait, and backcrossing the selected F1 progeny plant to a plantof soybean variety XB39N05. This method may further comprise the step ofobtaining a molecular marker profile of soybean variety XB39N05 andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of XB39N05. In oneembodiment the desired trait is a mutant gene or transgene present inthe donor parent.

Recurrent Selection and Mass Selection

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. XB39N05 is suitable for use in arecurrent selection program. The method entails individual plants crosspollinating with each other to form progeny. The progeny are grown andthe superior progeny selected by any number of selection methods, whichinclude individual plant, half-sib progeny, full-sib progeny and selfedprogeny. The selected progeny are cross pollinated with each other toform progeny for another population. This population is planted andagain superior plants are selected to cross pollinate with each other.Recurrent selection is a cyclical process and therefore can be repeatedas many times as desired. The objective of recurrent selection is toimprove the traits of a population. The improved population can then beused as a source of breeding material to obtain new varieties forcommercial or breeding use, including the production of a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected varieties.

Mass selection is a useful technique when used in conjunction withmolecular marker enhanced selection. In mass selection seeds fromindividuals are selected based on phenotype or genotype. These selectedseeds are then bulked and used to grow the next generation. Bulkselection requires growing a population of plants in a bulk plot,allowing the plants to self-pollinate, harvesting the seed in bulk andthen using a sample of the seed harvested in bulk to plant the nextgeneration. Also, instead of self pollination, directed pollinationcould be used as part of the breeding program.

Mutation Breeding

Mutation breeding is another method of introducing new traits intosoybean variety XB39N05. Mutations that occur spontaneously or areartificially induced can be useful sources of variability for a plantbreeder. The goal of artificial mutagenesis is to increase the rate ofmutation for a desired characteristic. Mutation rates can be increasedby many different means including temperature, long-term seed storage,tissue culture conditions, radiation; such as X-rays, Gamma rays (e.g.cobalt 60 or cesium 137), neutrons, (product of nuclear fission byuranium 235 in an atomic reactor), Beta radiation (emitted fromradioisotopes such as phosphorus 32 or carbon 14), or ultravioletradiation (preferably from 2500 to 2900 nm), or chemical mutagens (suchas base analogues (5-bromo-uracil), related compounds (8-ethoxycaffeine), antibiotics (streptonigrin), alkylating agents (sulfurmustards, nitrogen mustards, epoxides, ethylenamines, sulfates,sulfonates, sulfones, lactones), azide, hydroxylamine, nitrous acid, oracridines. Once a desired trait is observed through mutagenesis thetrait may then be incorporated into existing germplasm by traditionalbreeding techniques. Details of mutation breeding can be found in“Principles of Cultivar Development” Fehr, 1993 Macmillan PublishingCompany. In addition, mutations created in other soybean plants may beused to produce a backcross conversion of XB39N05 that comprises suchmutation.

Breeding with Molecular Markers

Molecular markers, which includes markers identified through the use oftechniques such as Isozyme Electrophoresis, Restriction Fragment LengthPolymorphisms (RFLPs), Randomly Amplified Polymorphic DNAs (RAPDs),Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNA AmplificationFingerprinting (DAF), Sequence Characterized Amplified Regions (SCARs),Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats(SSRs) and Single Nucleotide Polymorphisms (SNPs), may be used in plantbreeding methods utilizing XB39N05.

Isozyme Electrophoresis and RFLPs have been widely used to determinegenetic composition. Shoemaker and Olsen, ((1993) Molecular Linkage Mapof Soybean (Glycine max L. Merr.). p. 6.131–6.138. In S. J. O'Brien(ed.) Genetic Maps: Locus Maps of Complex Genomes. Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y.), developed a moleculargenetic linkage map that consisted of 25 linkage groups with about 365RFLP, 11 RAPD (random amplified polymorphic DNA), three classicalmarkers, and four isozyme loci. See also, Shoemaker R. C. 1994 RFLP Mapof Soybean. P. 299–309 In R. L. Phillips and l. K. Vasil (ed.) DNA-basedmarkers in plants. Kluwer Academic Press Dordrecht, the Netherlands.

SSR technology is currently the most efficient and practical markertechnology; more marker loci can be routinely used and more alleles permarker locus can be found using SSRs in comparison to RFLPs. For exampleDiwan and Cregan, described a highly polymorphic microsatellite loci insoybean with as many as 26 alleles. (Diwan, N., and P. B. Cregan 1997Automated sizing of fluorescent-labeled simple sequence repeat (SSR)markers to assay genetic variation in Soybean Theor. Appl. Genet.95:220–225.) Single Nucleotide Polymorphisms may also be used toidentify the unique genetic composition of the invention and progenyvarieties retaining that unique genetic composition. Various molecularmarker techniques may be used in combination to enhance overallresolution.

Soybean DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Cregan et. al, “An Integrated Genetic Linkage Map of the SoybeanGenome” Crop Science 39:1464–1490 (1999). Sequences and PCR conditionsof SSR Loci in Soybean as well as the most current genetic map may befound in Soybase on the world wide web.

One use of molecular markers is Quantitative Trait Loci (QTL) mapping.QTL mapping is the use of markers, which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plant'sgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.

Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a soybean plant for which XB39N05 is a parent can be used toproduce double haploid plants. Double haploids are produced by thedoubling of a set of chromosomes (1N) from a heterozygous plant toproduce a completely homozygous individual. For example, see Wan et al.,“Efficient Production of Doubled Haploid Plants Through ColchicineTreatment of Anther-Derived Maize Callus”, Theoretical and AppliedGenetics, 77:889–892,1989 and US2003/0005479. This can be advantageousbecause the process omits the generations of selfing needed to obtain ahomozygous plant from a heterozygous source.

Thus, an embodiment of this invention is a process for making asubstantially homozygous XB39N05 progeny plant by producing or obtaininga seed from the cross of XB39N05 and another soybean plant and applyingdouble haploid methods to the F1 seed or F1 plant or to any successivefilial generation. Based on studies in maize and currently beingconducted in soybean, such methods would decrease the number ofgenerations required to produce a variety with similar genetics orcharacteristics to XB39N05. See Bernardo, R. and Kahler, A. L., Theor.Appl. Genet. 102:986–992, 2001.

In particular, a process of making seed retaining the molecular markerprofile of soybean variety XB39N05 is contemplated, such processcomprising obtaining or producing F1 seed for which soybean varietyXB39N05 is a parent, inducing doubled haploids to create progeny withoutthe occurrence of meiotic segregation, obtaining the molecular markerprofile of soybean variety XB39N05, and selecting progeny that retainthe molecular marker profile of XB39N05.

Use of XB39N05 in Tissue Culture

This invention is also directed to the use of variety XB39N05 in tissueculture. Tissue culture of various tissues of soybeans and regenerationof plants therefrom is well known and widely published. For example,reference may be had to Komatsuda, T. et al., “Genotype X SucroseInteractions for Somatic Embryogenesis in Soybean,” Crop Sci. 31:333–337(1991); Stephens, P. A. et al., “Agronomic Evaluation ofTissue-Culture-Derived Soybean Plants,” Theor. Appl. Genet. (1991)82:633–635; Komatsuda, T. et al., “Maturation and Germination of SomaticEmbryos as Affected by Sucrose and Plant Growth Regulators in SoybeansGlycine gracilis Skvortz and Glycine max (L.) Merr.,” Plant Cell, Tissueand Organ Culture, 28:103–113 (1992); Dhir, S. et al., “Regeneration ofFertile Plants from Protoplasts of Soybean (Glycine max L. Merr.):Genotypic Differences in Culture Response,” Plant Cell Reports (1992)11:285–289; Pandey, P. et al., “Plant Regeneration from Leaf andHypocotyl Explants of Glycine wightii (W. and A.) VERDC. var.longicauda,” Japan J. Breed. 42:1–5 (1992); and Shetty, K., et al.,“Stimulation of In Vitro Shoot Organogenesis in Glycine max (Merrill.)by Allantoin and Amides,” Plant Science 81:(1992) 245–251; as well asU.S. Pat. No. 5,024,944, issued Jun. 18, 1991 to Collins et al. and U.S.Pat. No. 5,008,200, issued Apr. 16, 1991 to Ranch et al., thedisclosures of which are hereby incorporated herein in their entirety byreference. Thus, another aspect of this invention is to provide cellswhich upon growth and differentiation produce soybean plants having thephysiological and morphological characteristics of soybean varietyXB39N05.

REFERENCES

-   Aukerman, M. J. et al. (2003) “Regulation of Flowering Time and    Floral Organ Identity by a MicroRNA and Its APETALA2-like Target    Genes” The Plant Cell 15:2730–2741-   Berry et al., Assessing Probability of Ancestry Using Simple    Sequence Repeat Profiles: Applications to Maize Inbred Lines and    Soybean Varieties” Genetics 165:331–342 (2003)-   Boppenmaier, et al., “Comparisons Among Strains of Inbreds for    RFLPs”, Maize Genetics Cooperative Newsletter, 65:1991, p. 90-   Conger, B. V., et al. (1987) “Somatic Embryogenesis From Cultured    Leaf Segments of Zea Mays”, Plant Cell Reports, 6:345–347-   Cregan et al, “An Integrated Genetic Linkage Map of the Soybean    Genome” Crop Science 39:1464–1490 (1999).-   Diwan et al., “Automated sizing of fluorescent-labeled simple    sequence repeat (SSR) markers to assay genetic variation in Soybean”    Theor. Appl. Genet. 95:220–225. (1997)-   Duncan, D. R., et al. (1985) “The Production of Callus Capable of    Plant Regeneration From Immature Embryos of Numerous Zea Mays    Genotypes”, Planta, 165:322–332-   Edallo, et al. (1981) “Chromosomal Variation and Frequency of    Spontaneous Mutation Associated with in Vitro Culture and Plant    Regeneration in Maize”, Maydica, XXVI:39–56-   Fehr, Walt, Principles of Cultivar Development, pp. 261–286 (1987)-   Green, et al. (1975) “Plant Regeneration From Tissue Cultures of    Maize”, Crop Science, Vol.15, pp. 417–421-   Green, C. E., et al. (1982) “Plant Regeneration in Tissue Cultures    of Maize” Maize for Biological Research, pp. 367–372-   Hallauer, A. R. et al. (1988) “Corn Breeding” Corn and Corn    Improvement, No. 18, pp. 463–481-   Lee, Michael (1994) “Inbred Lines of Maize and Their Molecular    Markers”, The Maize Handbook, Ch. 65:423–432-   Meghji, M. R., et al. (1984) “Inbreeding Depression, Inbred & Hybrid    Grain Yields, and Other Traits of Maize Genotypes Representing Three    Eras”, Crop Science, Vol. 24, pp. 545–549-   Openshaw, S. J., et al. (1994) “Marker-assisted selection in    backcross breeding”. pp. 41–43. In Proceedings of the Symposium    Analysis of Molecular Marker Data. 5–7 Aug. 1994. Corvallis, Oreg.,    American Society for Horticultural Science/Crop Science Society of    America-   Phillips, et al. (1988) “Cell/Tissue Culture and In Vitro    Manipulation”, Corn & Corn Improvement, 3rd Ed., ASA Publication,    No. 18, pp. 345–387-   Poehlman et al (1995) Breeding Field Crop, 4th Ed., Iowa State    University Press, Ames, Iowa., pp. 132–155 and 321–344-   Rao, K. V., et al., (1986) “Somatic Embryogenesis in Glume Callus    Cultures”, Maize Genetics Cooperative Newsletter, No. 60, pp. 64–65-   Sass, John F. (1977) “Morphology”, Corn & Corn Improvement, ASA    Publication, Madison, Wis. pp. 89–109-   Smith, J. S. C., et al., “The Identification of Female Selfs in    Hybrid Maize: A Comparison Using Electrophoresis and Morphology”,    Seed Science and Technology 14,1–8-   Songstad, D. D. et al. (1988) “Effect of    ACC(1-aminocyclopropane-1-carboyclic acid), Silver Nitrate &    Norbonadiene on Plant Regeneration From Maize Callus Cultures”,    Plant Cell Reports, 7:262–265-   Tomes, et al. (1985) “The Effect of Parental Genotype on Initiation    of Embryogenic Callus From Elite Maize (Zea Mays L.) Germplasm”,    Theor. Appl. Genet., Vol. 70, p. 505–509-   Troyer, et al. (1985) “Selection for Early Flowering in Corn: 10    Late Synthetics”, Crop Science, Vol. 25, pp. 695–697-   Umbeck, et al. (1983) “Reversion of Male-Sterile T-Cytoplasm Maize    to Male Fertility in Tissue Culture”, Crop Science, Vol. 23, pp.    584–588-   Wan et al., “Efficient Production of Doubled Haploid Plants Through    Colchicine Treatment of Anther-Derived Maize Callus”, Theoretical    and Applied Genetics, 77:889–892, 1989-   Wright, Harold (1980) “Commercial Hybrid Seed Production”,    Hybridization of Crop Plants, Ch. 8:161–176-   Wych, Robert D. (1988) “Production of Hybrid Seed”, Corn and Corn    Improvement, Ch. 9, pp. 565–607    Deposits

Applicant(s) have made a deposit of at least 2500 seeds of SoybeanVariety XB39N05 with the American Type Culture Collection (ATCC),Manassas, Va. 20110 USA, ATCC Deposit No. PTA-7685. The seeds to bedeposited with the ATCC on Jun. 30, 2006 were taken from the depositmaintained by Pioneer Hi-Bred International, Inc., 7250 NW 62^(nd)Avenue, Johnston, Iowa 50131 since prior to the filing date of thisapplication. Access to this deposit will be available during thependency of the application to the Commissioner of Patents andTrademarks and persons determined by the Commissioner to be entitledthereto upon request. Upon allowance of any claims in the application,the Applicant will make the deposit available to the public pursuant to37 C.F.R. §1.808. This deposit of Soybean Variety XB39N05 will bemaintained in the ATCC depository, which is a public depository, for aperiod of 30 years, or 5 years after the most recent request, or for theenforceable life of the patent, whichever is longer, and will bereplaced if it becomes nonviable during that period. Additionally,Applicant has or will satisfy all the requirements of 37 C.F.R.§§1.801–1.809, including providing an indication of the viability of thesample upon deposit. Applicant has no authority to waive anyrestrictions imposed by law on the transfer of biological material orits transportation in commerce. Applicant does not waive anyinfringement of their rights granted under this patent or under thePlant Variety Protection Act (7 USC 2321 et seq.).

TABLE 1 Variety Description Information XB39N05 Yield Potential YLD/RM 9Relative Maturity (RM) RM 39 Canadian HU CHU Herbicide Resistance RR,STS RR Harvest Standability LDGSEV 7 Field Emergence EMGSC 7 HypocotylLength HYPLSC 9 Hypocotyl Length L Phytophthora Gene PRGENE 1KPhytophthora Race 4 Resistant Phytophthora Race 7 Resistant PhytophthoraRace 25 Susceptible Phytophthora Field PRT 4 Tolerance Brown Stem RotBSR 9 Iron Chlorosis FEC 6 White Mold WHMD Cyst Nematode Race 1 SCN1 3Cyst Nematode Race 2 SCN2 Cyst Nematode Race 3 SCN3 8 Cyst Nematode Race5 SCN5 Cyst Nematode Race 14 SCN14 Sudden Death Syndrome SDS 7 Root-knotNematode- RKI Southern Root-knot Nematode - RKA Peanut Stem Canker CNKRFrogeye Leaf Spot FEY 9 Aerial Web Blight AERBLT Reduced Tillage NOTILLAdaptability Canopy Width (9 = wide) CW 6 Shattering SHATTR 8Height/Maturity (9 = tall) HGT/RM 8 Plant Habit HAB IndeterminateOil/Meal Type HLC, LST, LLC, LPA, HSC Seed Protein (% @ Dry PROT 38.43Wgt Basis) Seed Protein (% @ 13% PROTN 34.01 H2O) Seed Oil (% @ Dry WgtOILT 21.51 Basis) Seed Oil (% @ 13% OILPCT 19.04 H2O) Seed Size (avgseeds/lb) S/LB Seed Size Range SEEDSZRANG Flower Color FL PurplePubescence Color PU Light Tawny Hila Color HI Black Pod Color PD BrownSeed Coat Luster SCL Dull

TABLE 2 VARIETY COMPARISON DATA YIELD bu/a MATABS LDGSEV FEC score SDSscore OILPCT pct PROTN pct Statistic 60# ABS count ABS score ABS HGT inABS ABS ABS ABS ABS XB39N05 52.9 131.1 6.7 40 5 7 19 34.03 93M80 51130.7 6.4 40.9 4.2 5.4 19.4 33.86 #Locs 45 16 15 19 5 8 7 7 #Reps 76 2323 29 13 16 7 7 #Years 2 2 2 2 2 2 2 2 Abs. Diff 2 0.4 0.4 0.9 0.8 1.60.38 0.17 Prob 0.018 0.524 0.102 0.204 0.152 0.045 0.117 0.507 XB39N0553.2 131.1 6.7 40 5 7.2 19 34.03 93M90 52.1 131.5 8.2 39.6 2.7 7.6 1934.33 #Locs 48 16 15 19 5 9 7 7 #Reps 80 23 23 29 13 17 7 7 #Years 3 2 22 2 3 2 2 Abs. Diff 1.1 0.4 1.5 0.4 2.3 0.4 0.02 0.3 Prob 0.121 0.1910.000 0.571 0.004 0.452 0.905 0.465 XB39N05 56.6 128.1 6.7 37.9 5 6.718.8 34.18 93M92 55.7 127.2 6.7 34 5 5.9 19.2 34.29 #Locs 30 9 9 12 4 74 4 #Reps 62 16 17 22 11 15 4 4 #Years 1 1 1 1 1 1 1 1 Abs. Diff 0.8 0.90 3.9 0 0.8 0.39 0.12 Prob 0.497 0.261 1.000 0.000 0.954 0.329 0.2410.864 XB39N05 56.6 128.1 6.7 37.9 5 6.7 18.8 34.18 93M93 52.1 127.9 6.936.2 3.5 7.5 19 34.22 #Locs 30 9 9 12 4 7 4 4 #Reps 61 16 17 22 11 15 44 #Years 1 1 1 1 1 1 1 1 Abs. Diff 4.5 0.2 0.2 1.8 1.5 0.8 0.17 0.05Prob 0.000 0.634 0.548 0.012 0.117 0.130 0.654 0.914 XB39N05 56.6 128.16.7 37.9 5 7 18.8 34.18 94B13 54.8 128.8 7.1 36.8 3.5 7.2 18.5 33.74#Locs 33 9 9 12 4 8 4 4 #Reps 65 16 17 22 11 16 4 4 #Years 2 1 1 1 1 2 11 Abs. Diff 1.8 0.7 0.4 1.1 1.5 0.2 0.32 0.44 Prob 0.028 0.347 0.3360.013 0.112 0.797 0.198 0.326

TABLE 3 Soybean SSR Marker Set Markers Sctt008 Satt372 Satt495 Satt328Satt582 Satt523 Satt572 Satt389 Satt284 Satt165 Satt186 Satt513 Satt042Sct137 Satt590 Satt300 Satt598 Satt150 Satt050 Satt204 Satt567 Satt385Satt602 Satt540 Satt545 Satt452 Satt175 Satt225 Satt193 Satt551 Satt133Satt348 Satt250 Satt411 Satt144 Satt336 Satt233 Sat090 Satt255 Satt327Satt594 Satt234 Satt421 Satt517 Satt257 Satt470 Sat117 Satt358 Satt455Sct187 Satt259 Satt409 Satt568 Satt420 Satt228 Sctt009 Satt262 Sct188Satt279 Satt478 Satt353 Satt367 Satt592 Satt509 Satt127 Satt153 Satt251Sctt012 Satt216 Satt197 Satt270 Satt266 Satt213 Sct028 Satt412 Satt577Satt357 Satt546 Satt467 Satt221 Satt172 Sct034 Satt383 Sat104 Satt243Satt295 Satt440 Satt601 Satt507 Satt249 Satt556 Satt147 Sct046 Satt122Satt196 Satt596 Satt534 Satt380 Satt142 Satt183 Satt565 Satt431 Sct186Satt102 Satt451 Satt555 Satt227 Satt441 Satt432 Satt557 Satt457 Satt475

All publications, patents and patent applications mentioned in thespecification are indicative of the level of those skilled in the art towhich this invention pertains. All such publications, patents and patentapplications are incorporated by reference herein for the purpose citedto the same extent as if each was specifically and individuallyindicated to be incorporated by reference herein.

The foregoing invention has been described in detail by way ofillustration and example for purposes of clarity and understanding. Asis readily apparent to one skilled in the art, the foregoing are onlysome of the methods and compositions that illustrate the embodiments ofthe foregoing invention. It will be apparent to those of ordinary skillin the art that variations, changes, modifications and alterations maybe applied to the compositions and/or methods described herein withoutdeparting from the true spirit, concept and scope of the invention.

1. A seed of soybean variety XB39N05, representative seed of said soybean variety XB39N05 having been deposited under ATCC Accession Number PTA-7685.
 2. A soybean plant, or a part thereof, produced by growing the seed of claim
 1. 3. A part of the plant of claim 2, further defined as pollen, an ovule, or a cell.
 4. A soybean plant, or a part thereof, expressing all the physiological and morphological characteristics of soybean variety XB39N05, representative seed of said soybean variety having been deposited under ATCC Accession Number PTA-7685.
 5. A tissue culture produced from protoplasts or regenerable cells from the plant of claim
 2. 6. The tissue culture according to claim 5, wherein the cells or protoplasts are produced from a plant tissue selected from the group consisting of: leaf, pollen, cotyledon, hypocotyl, embryos, root, root tip, pod, flower, shoot and stem.
 7. A soybean plant regenerated from the tissue culture of claim 5 having all the morphological and physiological characteristics of soybean variety Xb39N05, representative seed of said soybean variety XB39N05 having been deposited under ATCC Accession Number PTA-7685.
 8. A method for producing a soybean seed comprising crossing two soybean plants and harvesting the resultant soybean seed, wherein at least one soybean plant is the soybean plant of claim
 2. 9. A method for producing hybrid soybean seed comprising crossing the soybean plant according to claim 2 with a second soybean plant and harvesting the resultant hybrid soybean seed.
 10. A method for producing a XB39N05 derived soybean plant, comprising: a. Crossing soybean variety Xb39N05, a sample of said soybean variety deposited under ATCC Accession Number PTA-7685, with a second soybean plant to yield progeny soybean seed; and b. Growing said progeny soybean seed to yield said XB39N05-derived soybean plant.
 11. The method of claim 10, wherein the second soybean plant is transgenic.
 12. A method of producing a herbicide resistant soybean plant comprising introducing a transgene conferring herbicide resistance into the plant of claim
 2. 13. A herbicide resistant soybean plant produced by the method of claim
 12. 14. The soybean plant of claim 13, wherein the transgene confers resistance to a herbicide selected from the group consisting of glyphosate, sulfonylurea, imidazolinone, glufosinate, phenoxy proprionic acid, cycloshexone, triazine, and benzonitrile.
 15. A method of producing a pest or insect resistant soybean plant comprising introducing a transgene conferring pest or insect resistance into the soybean plant of claim
 2. 16. A pest or insect resistant soybean plant produced by the method of claim
 15. 17. The soybean plant of claim 16, wherein the transgene encodes a Bacillus thuringiensis (Bt) endotoxin.
 18. A method of producing a disease resistant soybean plant comprising introducing a transgene conferring disease resistance into the soybean plant of claim
 2. 19. A disease resistant soybean plant produced by the method of claim
 18. 